BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008811.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 973,145 number of mapped reads = 627,235 (64.45%) number of supplementary alignments = 5,116 (0.53%) number of secondary alignments = 0 number of mapped bases = 42,145,428 bp number of sequenced bases = 42,124,897 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,949 duplication rate = 1.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7595 >>>>>>> ACTG content number of A's = 12,082,788 bp (28.68%) number of C's = 7,797,588 bp (18.51%) number of T's = 12,521,010 bp (29.72%) number of G's = 9,668,422 bp (22.95%) number of N's = 55,089 bp (0.13%) GC percentage = 41.46% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 385,820 number of insertions = 3,602 mapped reads with insertion percentage = 0.57% number of deletions = 11,408 mapped reads with deletion percentage = 1.8% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 0.0136X std coverageData = 0.188X There is a 1.29% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3017324 0.012105582677765927 0.3813371221161028 chr2 243199373 4408897 0.0181287350605135 0.19762635905150475 chr3 198022430 2916396 0.014727604342598967 0.12624740229422687 chr4 191154276 2689539 0.01406999129854673 0.1274995534050927 chr5 180915260 2904329 0.016053532465973297 0.13036840687561982 chr6 171115067 2405739 0.014059188604355921 0.13265983446385396 chr7 159138663 2000491 0.012570741529982566 0.23206235778943052 chr8 146364022 2105964 0.014388536002379054 0.18817380973483894 chr9 141213431 1491831 0.010564370466998993 0.15454422087158587 chr10 135534747 1920453 0.014169451321586191 0.18110652085827605 chr11 135006516 2233210 0.01654149789333131 0.1702319496102933 chr12 133851895 1511933 0.011295566641025143 0.11112175068436031 chr13 115169878 1229207 0.010672990380349278 0.10536547626592228 chr14 107349540 1244520 0.011593156337698326 0.11953809300327531 chr15 102531392 1488948 0.014521874432368966 0.1260323867408068 chr16 90354753 1368293 0.015143564168671901 0.14059922560345134 chr17 81195210 1172189 0.014436676744847388 0.1337262318230299 chr18 78077248 1053071 0.01348755273751452 0.31083563778249257 chr19 59128983 770004 0.013022446200368439 0.25539492206788356 chr20 63025520 567588 0.009005685316043406 0.10232704716196625 chr21 48129895 571337 0.011870730239490446 0.11787606995196394 chr22 51304566 523588 0.010205485414300162 0.10361935592471007 chrMT 16571 4348 0.2623860961921429 0.5353177422294847 chrX 155270560 2416743 0.015564721348335447 0.13628174125655623 chrY 59373566 129486 0.0021808695135474934 0.07006058246761797